Package: RTCGAToolbox 2.37.0

Marcel Ramos

RTCGAToolbox: A new tool for exporting TCGA Firehose data

Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.

Authors:Mehmet Samur [aut], Marcel Ramos [aut, cre], Ludwig Geistlinger [ctb]

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RTCGAToolbox.pdf |RTCGAToolbox.html✨
RTCGAToolbox/json (API)
NEWS

# Install 'RTCGAToolbox' in R:
install.packages('RTCGAToolbox', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mksamur/rtcgatoolbox/issues

Datasets:
  • accmini - A subset of the Adrenocortical Carcinoma (ACC) dataset

On BioConductor:RTCGAToolbox-2.37.0(bioc 3.21)RTCGAToolbox-2.36.0(bioc 3.20)

differentialexpressiongeneexpressionsequencing

9.62 score 17 stars 5 packages 74 scripts 769 downloads 22 mentions 15 exports 99 dependencies

Last updated 17 days agofrom:c9d5508173. Checks:OK: 3 NOTE: 2 WARNING: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winOKOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:biocExtractgetBroadSubtypesgetDatagetFirehoseAnalyzeDatesgetFirehoseDatagetFirehoseDatasetsgetFirehoseRunningDatesgetGISTICPeaksgetLinksgetMutationRateisEmptymakeSummarizedExperimentFromGISTICselectTypeshowResultsupdateObject

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicliprcodetoolscpp11crayoncurldata.tableDBIDelayedArraydplyrfansifastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicDataCommonsGenomicFeaturesGenomicRangesgluehmshttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6RaggedExperimentrappdirsRCurlreadrrestfulrRhtslibrjsonRJSONIOrlangRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsselectrsnowSparseArraystringistringrSummarizedExperimentsysTCGAutilstibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXMLxml2XVectoryamlzlibbioc

RTCGAToolbox

Mehmet Kemal Samur

Rendered fromRTCGAToolbox-vignette.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-10-09
Started: 2015-03-31

Readme and manuals

Help Manual

Help pageTopics
A subset of the Adrenocortical Carcinoma (ACC) datasetaccmini
Extract and convert data from a 'FirehoseData' object to a 'Bioconductor' objectbiocExtract
An S4 class to store correlations between gene expression level and copy number dataCorResult-class
An S4 class to store differential gene expression resultsDGEResult-class
An S4 class to store data from CGA platformsFirehoseCGHArray-class
An S4 class to store main data object from clinent function.FirehoseData-class getData,ANY-method getData,FirehoseData-method getData,FirehoseGISTIC-method selectType,FirehoseData-method show,FirehoseData-method updateObject,FirehoseData-method
An S4 class to store processed copy number data. (Data processed by using GISTIC2 algorithm)FirehoseGISTIC-class isEmpty,FirehoseGISTIC-method updateObject,FirehoseGISTIC-method
An S4 class to store data from methylation platformsFirehoseMethylationArray-class
An S4 class to store data from array (mRNA, miRNA etc.) platformsFirehosemRNAArray-class
Download expression-based cancer subtypes from the Broad InstitutegetBroadSubtypes
Extract data from FirehoseData objectgetData
Get data analyze dates.getFirehoseAnalyzeDates
Get data from Firehose portal.getFirehoseData
Get a list of TCGA disease cohortsgetFirehoseDatasets
Get standard data running dates.getFirehoseRunningDates
Download GISTIC2 peak-level data from the Firehose pipelinegetGISTICPeaks
Get resource links from inputsgetLinks
Make a table for mutation rate of each gene in the cohortgetMutationRate
Gene coordinates for circle plot.hg19.ucsc.gene.locations
Create a SummarizedExperiment from FireHose GISTICmakeSummarizedExperimentFromGISTIC
RTCGAToolbox: A New Tool for Exporting TCGA Firehose DataRTCGAToolbox
Accessor function for the FirehoseData objectselectType
Export toptable or correlation data frameshowResults
Export toptable or correlation data frameshowResults,CorResult,CorResult-method showResults,CorResult-method
Export toptable or correlation data frameshowResults,DGEResult,DGEResult-method showResults,DGEResult-method